Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 359 bits (921), Expect = e-103 Identities = 191/468 (40%), Positives = 270/468 (57%), Gaps = 2/468 (0%) Query: 9 TQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH 68 T+ I+GEW DA SG+T+ + NPAT + I V G + A+AAA++ AWR + A Sbjct: 11 TKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPAWRALTAK 70 Query: 69 ERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRI 128 ER A +R+ L+ E AD +A +MT EQGKPL EA+ EV+ AA IEWFA+E +R+YG Sbjct: 71 ERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAEEAKRLYGDT 130 Query: 129 VPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPA 188 +P + V+K+ VG AA TPWNFP + RK ALA GC+ +VK +TP + Sbjct: 131 IPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTAL 190 Query: 189 ALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMK 248 AL +AG+P GV +V GD I + L +PV+RK++FTGST VG +L +K Sbjct: 191 ALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQQCAPTLK 250 Query: 249 RATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALV 308 + ++ELGG+AP IV DAD+ AV+ A +K+RNAGQ C+ R V + + D F + L Sbjct: 251 KVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYDAFAQKLA 310 Query: 309 KHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAP 368 LKVGNG E G T G L N L + S + +A GA++ GG+ +G GNF P Sbjct: 311 AAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPLG--GNFMEP 368 Query: 369 TVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLT 428 ++ NV V E FGP+A + F +++ I +AN FGLA Y + R + + + Sbjct: 369 AIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDISLIWKVA 428 Query: 429 QRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 + LE GM+ +N PFGG+K SG G EG ++ Y+ K + Sbjct: 429 EALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYI 476 Lambda K H 0.318 0.134 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 594 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 481 Length of database: 480 Length adjustment: 34 Effective length of query: 447 Effective length of database: 446 Effective search space: 199362 Effective search space used: 199362 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory